data_2WBJ # _model_server_result.job_id 0S3fqstQj4dyNCbtPANCOw _model_server_result.datetime_utc '2024-11-16 11:52:21' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2wbj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1186}' # _entry.id 2WBJ # _exptl.entry_id 2WBJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2WBJ _cell.length_a 109.706 _cell.length_b 130.271 _cell.length_c 180.22 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WBJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,J,K,L,M 1 1 E,F,G,H,I,N,O,P 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 J N N ? 6 K N N ? 6 N N N ? 6 O N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 5 n I NAG 1 I 1 NAG E 1181 NAG 5 n I NAG 2 I 2 NAG E 1182 NAG 5 n I BMA 3 I 3 BMA E 1183 BMA 5 n I MAN 4 I 4 MAN E 1184 MAN 5 n I MAN 5 I 5 MAN E 1185 MAN # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 107 A CYS 107 1_555 A SG CYS 163 A CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 15 B CYS 15 1_555 B SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 B SG CYS 117 B CYS 117 1_555 B SG CYS 173 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 C SG CYS 23 C CYS 23 1_555 C SG CYS 89 C CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 135 C CYS 135 1_555 C SG CYS 185 C CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 D SG CYS 46 D CYS 45 1_555 D SG CYS 117 D CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf7 D SG CYS 172 D CYS 171 1_555 D SG CYS 237 D CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 E SG CYS 107 E CYS 107 1_555 E SG CYS 163 E CYS 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 F SG CYS 15 F CYS 15 1_555 F SG CYS 79 F CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 F SG CYS 117 F CYS 117 1_555 F SG CYS 173 F CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf11 G SG CYS 23 G CYS 23 1_555 G SG CYS 89 G CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 G SG CYS 135 G CYS 135 1_555 G SG CYS 185 G CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf13 H SG CYS 46 H CYS 45 1_555 H SG CYS 117 H CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf14 H SG CYS 172 H CYS 171 1_555 H SG CYS 237 H CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 78 A ASN 78 1_555 J C1 NAG . A NAG 1181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 B ND2 ASN 19 B ASN 19 1_555 K C1 NAG . B NAG 1189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 E ND2 ASN 78 E ASN 78 1_555 N C1 NAG . E NAG 1186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale4 E ND2 ASN 118 E ASN 118 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 F ND2 ASN 19 F ASN 19 1_555 O C1 NAG . F NAG 1191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 I O3 BMA . I BMA 3 1_555 I C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 I O6 BMA . I BMA 3 1_555 I C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 NAG sing 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 2WBJ _atom_sites.fract_transf_matrix[1][1] 0.009115 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007676 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005549 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code J 6 NAG A 1 1181 1181 NAG NAG . K 6 NAG B 1 1189 1189 NAG NAG . L 7 SO4 B 1 1190 1190 SO4 SO4 . M 7 SO4 C 1 1201 1201 SO4 SO4 . N 6 NAG E 1 1186 1186 NAG NAG . O 6 NAG F 1 1191 1191 NAG NAG . P 7 SO4 F 1 1192 1192 SO4 SO4 . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 NAG . . . N 6 36.54 -11.54 35.467 1 94.71 ? C1 NAG 1186 E 1 HETATM 2 C C2 NAG . . . N 6 37.865 -12.297 35.674 1 100.72 ? C2 NAG 1186 E 1 HETATM 3 C C3 NAG . . . N 6 37.685 -13.616 36.44 1 99.86 ? C3 NAG 1186 E 1 HETATM 4 C C4 NAG . . . N 6 36.726 -13.501 37.627 1 98.89 ? C4 NAG 1186 E 1 HETATM 5 C C5 NAG . . . N 6 35.444 -12.774 37.203 1 99.28 ? C5 NAG 1186 E 1 HETATM 6 C C6 NAG . . . N 6 34.441 -12.618 38.348 1 97.62 ? C6 NAG 1186 E 1 HETATM 7 C C7 NAG . . . N 6 39.669 -12.026 34.005 1 104.19 ? C7 NAG 1186 E 1 HETATM 8 C C8 NAG . . . N 6 39.727 -11.508 32.594 1 103.48 ? C8 NAG 1186 E 1 HETATM 9 N N2 NAG . . . N 6 38.509 -12.569 34.394 1 102.85 ? N2 NAG 1186 E 1 HETATM 10 O O3 NAG . . . N 6 38.936 -14.072 36.903 1 100.31 ? O3 NAG 1186 E 1 HETATM 11 O O4 NAG . . . N 6 36.437 -14.793 38.117 1 95.52 ? O4 NAG 1186 E 1 HETATM 12 O O5 NAG . . . N 6 35.777 -11.499 36.668 1 98.95 ? O5 NAG 1186 E 1 HETATM 13 O O6 NAG . . . N 6 34.868 -11.618 39.247 1 96.12 ? O6 NAG 1186 E 1 HETATM 14 O O7 NAG . . . N 6 40.664 -11.944 34.729 1 103.69 ? O7 NAG 1186 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 130 _model_server_stats.query_time_ms 464 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #